Typhoon Tembin, with winds of up to 83 kilometres per hour, made landfall at the southern city of Suncheon and brought more than 150 millimetres of rain to some parts of the country, the weather service said.
The transport ministry said 173 domestic and international flights had been cancelled. Schools were closed or class hours adjusted, mainly in southern areas.
Scores of sea ferry routes were shut in the south and southwestern regions.
Tembin was moving northeast through southern provinces at a speed of 24 km per hour and was forecast to arrive at the Sea of Japan (East Sea) late today.
On Tuesday Typhoon Bolaven – the strongest to hit the country for almost a decade – left a trail of death and damage across parts of the country.
It drove two Chinese fishing ships with a total crew of 33 aground off the southern coast of Jeju. Rescuers pulled a total of 12 people to safety, and six swam ashore.
Nine bodies had been recovered as of today, leaving six still missing.
The hunt for the six was briefly suspended when Typhoon Tembin approached but later resumed despite high waves. Ten divers and a helicopter were taking part, said Ko Chang-Keon, a coastguard spokesman in Jeju.
The confirmed death toll from Typhoon Bolaven, including South Koreans killed elsewhere due to the storm, is now 19. Bolaven moved on to North Korea, damaging crops and toppling thousands of trees.